Aikido is supposed to be a martial art. Not a religion. Although it has spiritual aspects, it is not in anyway religious. O-Sensei's religious beliefs may have helped him to find the Art of Peace but he did not in anyway impose his beliefs into the practice of Aikido.

If westerners were to impose their religious beliefs to make the spiritual part of Aikido more understandable, then it would be ruining the whole practice of it.

The clapping and bowing at the beginning of class is supposed to be respect to O-Sensei and to show that your mind is ready to learn Aikido for that class. At the end of class it is a respect and thanks for the knowledge and ancestors of Aikido.